This depends on the platform of choice. For example, Sequencing Facility at ATRF, Frederick, typically uses 1 X 75 for running ChIP-seq samples. The first number (1) denotes single-end and the second number (75) means that the each read will be 75 bases long. One should remember that each read may undergo different amount of adapter removal and/or quality-based trimming, which may reduce its length. Hence, the average read-length post trimming will be < 75bp for this example. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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